Next generation sequencing in patients with nephrolithiasis: how does it perform compared with standard urine and stone cultures?
bacteriuria
infection
nephrolithiasis
next generation sequencing
Journal
Therapeutic advances in urology
ISSN: 1756-2872
Titre abrégé: Ther Adv Urol
Pays: England
ID NLM: 101487328
Informations de publication
Date de publication:
Historique:
received:
06
11
2020
accepted:
11
01
2021
entrez:
8
3
2021
pubmed:
9
3
2021
medline:
9
3
2021
Statut:
epublish
Résumé
Our aim was to compare microorganism detection between standard culture (Ctx) and next generation sequencing (NGS) in patients undergoing surgery for nephrolithiasis; we prospectively compared both urine and stone culture results using these two techniques. We prospectively compared microorganism detection of urine and stone cultures using Ctx We prospectively evaluated 84 patients. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of Voided Ctx predicting Stone Ctx were 66.7%, 73.7%, 54.5%, and 82.4%, respectively. Concordance of Voided Ctx microorganisms to Stone microorganisms decreased when NGS was used for the Stone compared with Ctx. The sensitivity, specificity, PPV, and NPV of Voided NGS to predict Stone Ctx microorganisms were 85.2%, 24.6%, 34.8%, and 77.8%, respectively. The concordance of Voided NGS to Stone microorganisms improved when the Stone was analyzed NGS has a higher detection rate of microorganisms than standard culture for both preoperative urine and stone cultures. Voided NGS was the most sensitive in predicting a positive Stone sample, but the specificity and PPV were, overall, low. Further correlation of NGS microorganism detection with patient outcomes will determine which clinical situations may benefit most from NGS
Sections du résumé
BACKGROUND
BACKGROUND
Our aim was to compare microorganism detection between standard culture (Ctx) and next generation sequencing (NGS) in patients undergoing surgery for nephrolithiasis; we prospectively compared both urine and stone culture results using these two techniques.
METHODS
METHODS
We prospectively compared microorganism detection of urine and stone cultures using Ctx
RESULTS
RESULTS
We prospectively evaluated 84 patients. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of Voided Ctx predicting Stone Ctx were 66.7%, 73.7%, 54.5%, and 82.4%, respectively. Concordance of Voided Ctx microorganisms to Stone microorganisms decreased when NGS was used for the Stone compared with Ctx. The sensitivity, specificity, PPV, and NPV of Voided NGS to predict Stone Ctx microorganisms were 85.2%, 24.6%, 34.8%, and 77.8%, respectively. The concordance of Voided NGS to Stone microorganisms improved when the Stone was analyzed
CONCLUSION
CONCLUSIONS
NGS has a higher detection rate of microorganisms than standard culture for both preoperative urine and stone cultures. Voided NGS was the most sensitive in predicting a positive Stone sample, but the specificity and PPV were, overall, low. Further correlation of NGS microorganism detection with patient outcomes will determine which clinical situations may benefit most from NGS
Identifiants
pubmed: 33680094
doi: 10.1177/1756287221994972
pii: 10.1177_1756287221994972
pmc: PMC7900788
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1756287221994972Informations de copyright
© The Author(s), 2021.
Déclaration de conflit d'intérêts
Conflict of interest statement: Dr Krambeck is a consultant for Boston Scientific and Lumenis and is on the data safety monitoring board for Sonomotion. Dr Rivera is a consultant for Boston Scientific and Lumenis. Dr Large is a consultant for Boston Scientific and Lumenis. No other disclosures or competing financial interests exist.
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